Buggy code:
public IPackageFragment findPackageFragment0 ( IPath path ) throws JavaModelException { } public IPackageFragmentRoot findPackageFragmentRoot ( IPath path ) throws JavaModelException { } public IPackageFragmentRoot findPackageFragmentRoot0 ( IPath path ) throws JavaModelException { } public IPackageFragmentRoot [ ] findPackageFragmentRoots ( IClasspathEntry entry ) { } public IType findType ( String fullyQualifiedName ) throws JavaModelException { } public IType findType ( String packageName , String typeQualifiedName ) throws JavaModelException { } protected void flushClasspathProblemMarkers ( boolean flushCycleMarkers , boolean flushClasspathFormatMarkers ) { } protected boolean generateInfos ( OpenableElementInfo info , IProgressMonitor pm , Map newElements , IResource underlyingResource ) throws JavaModelException { } public IPackageFragmentRoot [ ] getAllPackageFragmentRoots ( ) throws JavaModelException { } public IClasspathEntry getClasspathEntryFor ( IPath path ) throws JavaModelException { } public IMarker getCycleMarker ( ) { } public IClasspathEntry [ ] getExpandedClasspath ( boolean ignoreUnresolvedVariable ) throws JavaModelException { } public IClasspathEntry [ ] getExpandedClasspath ( boolean ignoreUnresolvedVariable , boolean generateMarkerOnError ) throws JavaModelException { } protected char getHandleMementoDelimiter ( ) { } private ICommand getJavaCommand ( IProjectDescription description ) throws CoreException { } protected JavaProjectElementInfo getJavaProjectElementInfo ( ) throws JavaModelException { } public NameLookup getNameLookup ( ) throws JavaModelException { } public Object [ ] getNonJavaResources ( ) throws JavaModelException { } public String getOption ( String optionName , boolean inheritJavaCoreOptions ) { } public Map getOptions ( boolean inheritJavaCoreOptions ) { } public IPath getOutputLocation ( ) throws JavaModelException { } public IPackageFragmentRoot getPackageFragmentRoot ( IPath path ) { } public IPackageFragmentRoot getFolderPackageFragmentRoot ( IPath path ) { } public IPackageFragmentRoot getPackageFragmentRoot ( IResource resource ) { } public IPackageFragmentRoot getPackageFragmentRoot ( String jarPath ) { } public IPackageFragmentRoot getPackageFragmentRoot0 ( IPath jarPath ) { } public IPackageFragmentRoot [ ] getPackageFragmentRoots ( ) throws JavaModelException { } public IPackageFragmentRoot [ ] getPackageFragmentRoots ( IClasspathEntry entry ) { } protected IPackageFragmentRoot [ ] getPackageFragmentRoots ( IPath path ) throws JavaModelException { } public IPackageFragment [ ] getPackageFragments ( ) throws JavaModelException { } public IPackageFragment [ ] getPackageFragmentsInRoots ( IPackageFragmentRoot [ ] roots ) { } public IPath getPath ( ) { } public IProject getProject ( ) { } public Preferences getPreferences ( ) { } public IClasspathEntry [ ] getRawClasspath ( ) throws JavaModelException { } public String [ ] getRequiredProjectNames ( ) throws JavaModelException { } public IClasspathEntry [ ] getResolvedClasspath ( boolean ignoreUnresolvedEntry ) throws JavaModelException { } public IClasspathEntry [ ] getResolvedClasspath ( boolean ignoreUnresolvedEntry , boolean generateMarkerOnError ) throws JavaModelException { } public IClasspathEntry [ ] getResolvedClasspath ( IClasspathEntry [ ] classpathEntries , IPath projectOutputLocation , boolean ignoreUnresolvedEntry , boolean generateMarkerOnError , Map reverseMap ) throws JavaModelException { } public IResource getResource ( ) { } public ISearchableNameEnvironment getSearchableNameEnvironment ( ) throws JavaModelException { } public String getSharedProperty ( String key ) throws CoreException { } public SourceMapper getSourceMapper ( ) { } public IResource getUnderlyingResource ( ) throws JavaModelException { } public boolean hasBuildState ( ) { } public boolean hasClasspathCycle ( IClasspathEntry [ ] preferredClasspath ) { } public boolean hasCycleMarker ( ) { } public int hashCode ( ) { } public static boolean hasJavaNature ( IProject project ) { } public boolean hasSource ( ) { } public boolean isClasspathEqualsTo ( IClasspathEntry [ ] newClasspath , IPath newOutputLocation , IClasspathEntry [ ] otherClasspathWithOutput ) throws JavaModelException { } public boolean isOnClasspath ( IJavaElement element ) { } private boolean isOnClasspath ( IPath path ) { } public boolean isOnClasspath ( IResource resource ) { } public Preferences loadPreferences ( ) { } public IEvaluationContext newEvaluationContext ( ) { } public ITypeHierarchy newTypeHierarchy ( IRegion region , IProgressMonitor monitor ) throws JavaModelException { } public ITypeHierarchy newTypeHierarchy ( IType type , IRegion region , IProgressMonitor monitor ) throws JavaModelException { } protected OpenableElementInfo openWhenClosed ( IProgressMonitor pm ) throws JavaModelException { } public String [ ] projectPrerequisites ( IClasspathEntry [ ] entries ) throws JavaModelException { } protected IClasspathEntry [ ] readClasspathFile ( boolean createMarker , boolean logProblems ) { } protected void removeFromBuildSpec ( String builderID ) throws CoreException { } public IJavaElement rootedAt ( IJavaProject project ) { } public String rootID ( ) { } public boolean saveClasspath ( IClasspathEntry [ ] newClasspath , IPath newOutputLocation ) throws JavaModelException { } private void savePreferences ( Preferences preferences ) { } private void setJavaCommand ( IProjectDescription description , ICommand newCommand ) throws CoreException { } public void setOptions ( Map newOptions ) { } public void setOutputLocation ( IPath path , IProgressMonitor monitor ) throws JavaModelException { } public void setPreferences ( Preferences preferences ) { } public void setProject ( IProject project ) { } public void setRawClasspath ( IClasspathEntry [ ] entries , IPath outputLocation , IProgressMonitor monitor ) throws JavaModelException { } public void setRawClasspath ( IClasspathEntry [ ] newEntries , IPath newOutputLocation , IProgressMonitor monitor , boolean canChangeResource , IClasspathEntry [ ] oldResolvedPath , boolean needValidation , boolean needSave ) throws JavaModelException { JavaModelManager manager = ( ( JavaModelManager ) ( JavaModelManager . getJavaModelManager ( ) ) ) ; try { IClasspathEntry [ ] newRawPath = newEntries ; if ( newRawPath == null ) { newRawPath = defaultClasspath ( ) ; } SetClasspathOperation op = new SetClasspathOperation ( this , oldResolvedPath , newRawPath , newOutputLocation , canChangeResource , needValidation , needSave ) ; runOperation ( op , monitor ) ; } catch ( JavaModelException e ) { <START_BUG> manager . flush ( ) ; <END_BUG> throw e ; } } public void setRawClasspath ( IClasspathEntry [ ] entries , IProgressMonitor monitor ) throws JavaModelException { } protected void setRawClasspath0 ( IClasspathEntry [ ] rawEntries ) throws JavaModelException { } public void setSharedProperty ( String key , String value ) throws CoreException { } public static void updateAllCycleMarkers ( ) throws JavaModelException { } public void updateCycleParticipants ( IClasspathEntry [ ] preferredClasspath , ArrayList prereqChain , HashSet cycleParticipants , IWorkspaceRoot workspaceRoot , HashSet traversed ) { } public void updatePackageFragmentRoots ( ) { } }

Fix:
manager . deltaProcessor . flush ( ) ;